Most QuickBooks advice is a tour of features. These tips come from the other end: the problems we find when a business hands us a QuickBooks Online file that has drifted for a year or two. Each one is a habit that would have saved the owner a cleanup.
1. Reconcile to the bank statement, not to the feed
Matching transactions in the bank feed is not the same as reconciling. Feeds miss transactions, import the same one twice after a reconnection, and occasionally pick up items that never cleared. A reconciliation starts from the ending balance printed on the statement and proves the books agree with it.
Do it every month, for every bank account, credit card and loan. When an account will not tie, that is not a nuisance to force through. It is the earliest warning you will get that something in the file is wrong.
2. Use bank rules only where the answer never changes
Rules are useful for transactions that are always the same: rent, a software subscription, a loan payment. They are dangerous for vendors you pay for different reasons, such as a marketplace where you buy both office supplies and inventory. A wrong rule does not fail loudly. It miscodes the same way every month until somebody runs a report and wonders why supplies tripled.
If you use rules, have them suggest a category for review rather than add transactions automatically.
3. Record payment processor sales gross, not net
Stripe, Square, PayPal and Shopify deposit what is left after fees, refunds and chargebacks. Booking that deposit as income understates your revenue and hides what the processor is costing you. Record the gross sales, record the fees as an expense, record refunds on their own, and reconcile the processor's balance the same way you reconcile a bank account.
This is the single most common reason we see revenue in QuickBooks that does not match the sales reports the owner looks at every day.
4. Clear Payments to deposit every month
When you receive payment on an invoice, QuickBooks Online often holds it in an account called Payments to deposit (Undeposited Funds in older files and in QuickBooks Desktop) until you record the deposit. If the deposit then arrives in the bank feed and gets categorized as new income, the sale is counted twice.
Match the bank deposit to the payments it contains instead. At month end the account should hold only money you have genuinely received and not yet banked.
5. Connect each app once, and decide which one records the sale
A store connector posts the sale. The bank feed brings in the deposit for the same sale. Categorize both and revenue doubles. The same thing happens with bill pay and expense tools.
For each app, decide whether it creates the transaction in QuickBooks or whether the bank feed does. Then make sure the other one only matches. If you are not sure how an integration is set up, run a sales report for one week and compare it to the app's own numbers.
6. Keep the chart of accounts short
The setup wizard gives every business a generic chart of accounts, and it grows from there: an account added for a one-off purchase, a duplicate with a slightly different name, a "Miscellaneous" that ends up holding a fifth of all spending. Reports built on that structure cannot answer the questions you actually have.
Before adding an account, ask which report question it answers. Make unused accounts inactive, and merge the duplicates.
7. Do not leave a balance in Opening Balance Equity
QuickBooks puts amounts in Opening Balance Equity when something is entered without a clear other side: a starting balance, an account added mid-year, a reconciliation that was forced to tie. Once a file is set up properly, this account should be zero. A balance that grows over time means the file is absorbing errors rather than fixing them.
8. Keep owner money out of income and expenses
Personal purchases on the business card are not business expenses, and money you put into the business is not revenue. Record them in the equity accounts that fit your type of business, such as owner draws and contributions. Mixing them in inflates both sides of the profit and loss and hands your tax preparer numbers they have to unpick before they can use them.
9. Edit or void instead of deleting, and set a closing date
Deleting a transaction that was part of a past reconciliation breaks that reconciliation, often without anyone noticing until the next one will not tie. Edit or void it instead.
Once a month is reconciled and reviewed, set a closing date in QuickBooks Online's advanced accounting settings, with a password, so nothing in a closed month changes by accident. The audit log will show you who changed what if something does.
10. Give everyone their own login
Shared logins make the audit log useless, because every change looks like it came from the same person. Give each person their own user with the access they need, and invite your accountant or bookkeeper as an accountant user rather than handing over your own password.
How we use this list
When Feather takes over a QuickBooks file, the first month starts with exactly these checks. For monthly clients they are built into every close, which is why the monthly reports we send can be relied on. We are certified QuickBooks ProAdvisors, and most of our work is in QuickBooks Online.
If you read this list and recognized several of these in your own file, that is what our QuickBooks consulting and cleanup work is for. We do it remotely for businesses anywhere in the US, and our pages for Dallas, Atlanta, Miami and Denver describe what a cleanup looks like for the kinds of businesses in those cities. If the file is months behind as well, start with catch-up bookkeeping. Either way, a short call is enough for us to tell you what we would fix first.